Ahmad Affan Ali Murtadlo

Dendrobium lineale Rolfe is an important orchid species used as a parent in breeding. Currently, this orchid is classified as an endangered species and is listed in Appendix II according to CITES. This study aimed to investigate the effects of sucrose and coconut water (CW) on the asymbiotic seed germination and shoot development of this endangered Indonesian orchid. In vitro orchid seed culture aids in conservation and reintroduction. Three‐month‐old hand‐pollinated seeds were sown on Vacin and Went (VW) solid medium supplemented with several concentrations of sucrose (10, 20, and 30 g/L) or without sucrose (controls). Seed germination and protocorm development were investigated 1, 2, and 3 months after sowing. To analyze the role of CW in subsequent shoot development and root formation, shoots with an approximately 1‐cm length and comprising 1‐2 leaves obtained following seed germination were cultured on VW medium supplemented with several concentrations of CW (5%, 10%, 15%, and 20%) and without CW (control) treatment. After 4 months of culture, the number of roots, the number of leaves, and dry weight of the plantlets were recorded. VW medium containing 20 g/L sucrose effectively enhanced seed germination (89%) and shoot formation with one or more leaves (stage 5) (46%). Supplementation with 20% CW in VW medium was suitable for shoot development, resulting in well‐developed roots and leaves and improved fresh weight of plantlets compared with those in the other treatments. Moreover, 87% of the acclimatized plantlets survived. This protocol is an efficient method for the in vitro mass production and conservation of this endangered epiphytic orchid using asymbiotic seed culture.

Non-small cell lung cancer (NSCLC) presents a significant global health challenge, with its prevalence and mortality rates rising steadily. In Indonesia, Syzygium cumini (L.) Skeels, known for its flavonoid richness, has a long history in traditional medicine. However, its specific mechanisms of action against cancer, particularly in inducing apoptosis in NSCLC, have not been fully elucidated. This study utilized an in silico approach to evaluate the pro-apoptotic potential of S. cumini flavonoids against NSCLC by targeting key proteins: Bcl-2, Bax, and Caspase-3. We retrieved flavonoid structures from PubChem and protein data from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). The drug-likeness of these compounds was assessed using Swiss ADME, adhering to Lipinski's rule of five, while their anti-NSCLC probability was predicted using PASS Online. Molecular docking and screening were performed with PyRx, and the results were visualized using Discovery Studio. Our findings identified epigallocatechin 3-O-gallate and ellagic acid as the most promising anti-NSCLC candidates. Ellagic acid demonstrated the strongest binding affinity to Caspase-3, suggesting a potent pro-apoptotic effect. Epigallocatechin 3-O-gallate, on the other hand, exhibited the lowest binding energy across multiple target proteins, particularly Bcl-2 and Bax, indicating its broad pro-apoptotic potential. These results collectively suggest that flavonoids from S. cumini may hold significant promise as a source of novel anti-NSCLC agents, warranting further in vitro and in vivo investigations.

Context: Malaria remains a severe global health concern, exacerbated by increasing resistance to antimalarial agents in Plasmodium falciparum. Indonesian medicinal plants have demonstrated pharmacological potential, although their application against the calcium-dependent protein kinase 2 (CDPK2) of P. falciparum has not been previously explored. Aims: To assess the potential of Indonesian herbal compounds as inhibitors of P. falciparum CDPK2 using a range of in silico computational techniques. Methods: The structure of CDPK2 was retrieved from the Protein Data Bank (PDB ID: 4MVF) and prepared using the YASARA software. Structural validation was performed using Ramachandran plot analysis, ERRAT, and Verify 3D. The ligands were derived from documented Indonesian herbal compounds. Molecular docking was performed using AutoDock Vina integrated within YASARA, and the best-scoring ligands were subjected to DFT calculations using ORCA 5.0. ADME and biological activity predictions were performed using SwissADME and PASS, respectively. The stability of the most promising complex was assessed via normal mode analysis (NMA) using iMODS. Results: Among the screened compounds, epicatechin 3-O-(3-O-methylgallate) and remerin exhibited the highest binding affinities. While DFT analysis confirmed favorable electronic properties for both, remerin alone met the drug-likeness criteria based on ADME evaluation. Normal mode analysis demonstrated that the CDPK2-remerin complex maintained its structural stability throughout the simulation. Conclusions: Remerin was identified as a promising inhibitor of CDPK2 based on its binding affinity, pharmacokinetic properties, and molecular dynamics stability. Further in vitro and in vivo investigations are required to validate these findings.

Alizarin is a polycyclic compound isolated from roots of Rubia tinctorum that has potential as a breast anticancer candidate. Increasing anticancer activity can be done through structural modification to produce derivatives in the form of group substitution in the meta position using acyl. The purpose of this work is to forecast the anticancer activity of alizarin and its derivatives on the MMP-9 receptor using. Important biological activity factors will be identified by Quantitative Structure Activity molecular docking Relationship (QSAR) and projected absorption, distribution, metabolism, elimination, and toxicity (ADMET). Using Molegro Virtual Docker (MVD), molecular docking was carried out on the MMP 9 receptor (4WZV.pdb). LogP, Etot, and MR are the physicochemical parameters that are examined in order to produce QSAR. Statistical Package for the Social Science (SPSS) was used for the QSAR analysis. The pkCSM was utilized to determine ADMET prediction. The acyl alizarin derivatives have a lower rerank score than alizarin, according to the docking results so that they are predicted to have more potent anticancer activity. The QSAR analysis's findings indicated that logP and Etot had the greatest effects on the alizarin compound's and its derivatives' activity. The results of the ADMET prediction indicate that acyl alizarin is less harmful and superior to alizarin. Research findings show that it is possible to synthesize acyl alizarin derivatives, especially alizarin octanoate, which will then be tested in vitro or in vivo to determine its anti-breast cancer activity and toxicity.

Dengue virus (DENV) is still global problem and infecting millions of people a year. This virus belongs to Flavivirus and consists of the structural and non-structural proteins including envelop (E), capsid (C), NS2B/NS3, and NS5. Garcinia atroviridis Griff. ex T. Anders is traditional plant that has broad potential as antioxidant, antibacterial, and anti-cancer activities. However, the anti-DENV potential of this plant is uncertain. The objective of this research is to find out the potential of the phytochemical compounds of G. atroviridis as DENV antiviral drugs targeting E, C, NSB2/NS3, and NS5 proteins using molecular simulation approach. Sample retrieval was obtained from PubChem and RCSB PDB. Drug-likeness analysis has been assessed with Swiss ADME based on the pharmacology and pharmacokinetics aspects. Toxicity prediction was done by pkCSM webserver. PyRx was carried out to screen ligand-protein interaction virtually. Visualization of the best interaction was displayed by BIOVIA Discovery Studio. CABS-flex 2.0 version webserver was performed to predict stability interaction. Atroviridin was determined as the most promising as DENV antiviral to be tested by the wet laboratory approach.

Context: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread, causing a global pandemic with diverse symptoms and increased risk of mortality. Various symptoms and comorbidities contribute to a higher likelihood of death in patients. Additionally, existing antiviral drugs have shown incomplete efficacy. Rafflesia sp. and Sapria sp. are parasitic plants with potential medical applications as anti-SARS-CoV-2 agents. Aims: To evaluate the bioactive compounds derived from Rafflesia sp. and Sapria sp. as dual inhibitors against SARS-CoV-2. Methods: Ligand samples were obtained from the PubChem database. Target proteins essential for SARS-CoV-2 entry were obtained from the RCSB PDB. The antiviral potential of the bioactive compounds was evaluated using the Pass Online webserver. The bioactivity and inhibitory potential of selected ligands were analyzed using the SwissADME and Molinspiration web servers. In addition, a specific docking method was performed using PyRx software to determine binding activity and molecular interactions. Results: Computational analysis revealed that leucoanthocyanidin, ellagic acid, and catechin functioned as dual inhibitors, targeting angiotensin-converting enzyme 2 (ACE2), transmembrane protease serine 2 (TMPRSS2), furin, and cathepsin L for antiviral activity. However, valrubicin and diminazene, serving as control drugs for ACE2 and furin, respectively, demonstrated the most effective results through this mechanism. Further studies are required to validate these findings. Conclusions: The combination of bioactive compounds derived from Rafflesia sp. and Sapria sp. shows potential antiviral activity through a dual inhibitor mechanism involving leucoanthocyanidin, ellagic acid, and catechin, which target SARS-CoV-2 proteins, namely ACE2, TMPRSS2, furin, and cathepsin L.

There are no specific drugs or vaccines for Nipah virus (NiV), which is a new Paramyxovirus that infects swine and humans. This study was conducted to investigate B-cell epitope mapping of the NiV attachment glycoprotein and to construct peptide-based vaccine candidates using the reverse vaccinology approach. To generate the linear B-cell epitope, the NiV isolates were extractad from GenBank, NCBI, using the IEDB web server; peptide modeling was conducted using PEP-FOLD3; docking was conducted using PatchDock and FireDock; and in silico cloning was designed using SnapGene. Various peptides were successfully identified from the NiV attachment glycoprotein based on B-cell epitope prediction, allergenicity prediction, similarity prediction, and toxicity prediction. An in silico cloning design of the pET plasmic was also developed. The peptide “RFENTTSDKGKIPSKVIKSYYGTMDIKKINEGLLD” (1G peptide) is predicted to be a potential candidate for the NiV vaccine as it has several good vaccine characteristics. It increases the immune response of B cells through activation, differentiation into plasma cells, the formation of memory cells, and it may increase IgM/IgG antibody titres for viral neutralization. However, the results of this study should be further verified through in vivo and in vitro analyses

Human papillomavirus (HPV) is a small and non-enveloped deoxyribonucleic acid (DNA) virus that infected mucosal cells. This viral genome is composed of early and late genes. Late (L) encodes the L1 and L2 proteins. The structural protein L1 is located outside the virion. It contributes to the viral attachment mechanism; hence it becomes the target for multi-strain vaccine design. This review aims to discuss the potency of conserved L1 HPV region and the innovation of multi-strain vaccines for prevention strategies of HPV infection. Bioinformatics methods in vaccine design applied for identification of conserved sequences from databases, epitopes map, antigenicity test, prediction of similarity, and autoimmune level. The multi-strain vaccine innovation initiated in this review has more benefits compared to previous vaccines based on the level of vaccine coverage via conserved regions, potential of immune cell epitopes, antigenic properties, and possibility of autoimmune when produced. Therefore, the multi-strain HPV vaccines are predicted to be more effective than previous vaccines, including bivalent or quadrivalent. In conclusion, the strategy for expanding the prevention of HPV infection could be carried out by developing a new multi-strain-based vaccine by using conserved regions in L1 capsid from all virus strains to increase the protection.